本文整理匯總了Python中rgt.GenomicRegionSet.GenomicRegionSet.any_chrom方法的典型用法代碼示例。如果您正苦於以下問題：Python GenomicRegionSet.any_chrom方法的具體用法？Python GenomicRegionSet.any_chrom怎麽用？Python GenomicRegionSet.any_chrom使用的例子？那麽, 這裏精選的方法代碼示例或許可以為您提供幫助。您也可以進一步了解該方法所在類rgt.GenomicRegionSet.GenomicRegionSet的用法示例。
在下文中一共展示了GenomicRegionSet.any_chrom方法的1個代碼示例，這些例子默認根據受歡迎程度排序。您可以為喜歡或者感覺有用的代碼點讚，您的評價將有助於係統推薦出更棒的Python代碼示例。
示例1: read_bed
# 需要導入模塊: from rgt.GenomicRegionSet import GenomicRegionSet [as 別名]
# 或者: from rgt.GenomicRegionSet.GenomicRegionSet import any_chrom [as 別名]
def read_bed(self, bedfile, genome_file_dir):
"""Read the sequences defined by BED file on the given genomce"""
# Read BED into GenomicRegionSet
bed = GenomicRegionSet(os.path.basename(bedfile))
bed.read_bed(bedfile)
# Parse each chromosome and fetch the defined region in this chromosome
chroms = list(set(bed.get_chrom()))
chro_files = [x.split(".")[0] for x in os.listdir(genome_file_dir)]
for ch in chroms:
if ch not in chro_files: print(" *** There is no genome FASTA file for: "+ch)
# Read genome in FASTA according to the given chromosome
ch_seq = SequenceSet(name=ch, seq_type=SequenceType.DNA)
try:
ch_seq.read_fasta(os.path.join(genome_file_dir, ch+".fa"))
except:
continue
# Regions in given chromosome
beds = bed.any_chrom(chrom=ch)
for s in beds:
seq = ch_seq[0].seq[s.initial:s.final]
try: strand = s.strand
except: strand = "+"
self.sequences.append(Sequence(seq=seq, name=s.__repr__(),
strand=strand))